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ANIL RAJ

Stanford University, Department of Genetics


318 Campus Drive, Clark Bldg S240, MC 5444, Stanford, CA 94305

EDUCATION
Columbia University, Graduate School of Arts and Sciences
PhD. in Applied Physics and Applied Mathematics
Emphasis: Large-scale Machine Learning in Biology
M.Phil. in Applied Mathematics

October 2011
February 2009

Columbia University, School of Engineering and Applied Sciences


M.S. in Applied Physics

May 2006

Indian Institute of Technology Madras


B.Tech. in Aerospace Engineering / Physics

July 2005

PROFESSIONAL EXPERIENCE
Postdoctoral Scholar; Adviser: Dr. Jonathan Pritchard
Stanford University, Department of Genetics
University of Chicago, Department of Human Genetics
Graduate Research Assistant; Adviser: Dr. Chris Wiggins
Columbia University,
Department of Applied Physics and Applied Mathematics
Data Science Intern; Supervisor: Tom Quisel
OKCupid.com, New York

Aug 2013 Now


Sep. 2011 July 2013
May 2006 Aug 2011

June 2010 Aug 2010

Research Fellow; Adviser: Dr. N. Ananthakrishnan


Indian Institute of Technology Bombay,
Department of Aerospace Engineering

June 2004 Aug 2004

Research Assistant; Adviser: Dr. R. I. Sujith


Indian Institute of Technology Madras,
Department of Aerospace Engineering

Sep. 2002 May 2005

PEER-REVIEWED PUBLICATIONS (* equal contribution)


1. Anil Raj*, Sidney Wang*, Heejung Shim*, Arbel Harpak, Yang Li, Brett Englemann, Matthew
Stephens, Yoav Gilad, Jonathan K Pritchard. Thousands of novel translated open reading
frames in humans inferred by ribosome footprint profiling. Submitted to eLife
(http://biorxiv.org/content/early/2015/09/13/025874)
2. David A Knowles, Joe R Davis, Anil Raj, Xiaowei Zhu, James B Potash, Myrna M Weissman,
Jianxin Shi, Doug Levinson, Sara Mostafavi, Stephen B Montgomery, Alexis Battle. Allelespecific expression reveals interactions between genetic variation and environment.
Submitted to Nature Biotechnology (http://biorxiv.org/content/early/2015/09/13/025874)
3. Anil Raj*, Heejung Shim*, Yoav Gilad, Jonathan Pritchard, Matthew Stephens. (2015)
msCentipede: Modeling heterogeneity across genomic sites and replicates improves
accuracy in the inference of transcription factor binding, PLoS ONE 10(9): e0138030.

4. Anil Raj, Matthew Stephens, Jonathan Pritchard. (2014) Variational Inference of Population
Structure in Large SNP Datasets. Genetics, 197(2): 573-589
5. Graham McVicker, Bryce van de Geijn, Jacob Degner, Carolyn Cain, Nicholas Banovich, Anil
Raj, Noah Lewellen, Marsha Myrthil, Yoav Gilad, Jonathan Pritchard. (2013) Identification of
genetic variants that affect histone modification in human cells. Science, 342 (6159).
6. Anil Raj, Michael Dewar, Gustavo Palacios, Raul Rabadan and Chris Wiggins. (2011)
Identifying Hosts of Families of Viruses: A Machine Learning Approach. PLoS ONE 6(12):
e27631.
7. Anil Raj and Chris Wiggins. (2010) An information-theoretic derivation of min-cut based
clustering. IEEE Transactions on Pattern Analysis and Machine Intelligence, 32(6): 988-995.

OTHER PUBLICATIONS AND REPORTS


1. Anil Raj, Graham McVicker. (2014) The genome shows its sensitive side. Nature Methods,
11(1): 39-40
2. Anil Raj and Chris Wiggins. (2008) A non-negative expansion for small Jensen-Shannon
Divergences. 2008. (http://arxiv.org/abs/0810.5117)
3. Anil Raj and R. I. Sujith. (2005) Closed-form solutions for the free longitudinal vibration of
inhomogeneous rods. Journal of Sound and Vibration, 283(3-5).

AWARDS
RECOMB Travel Fellowship
Funded by Biogen Idec

2015

HackNY Fellowship
HackNY Initiative, New York
(http://hackny.org/a/2010/06/announcing-the-2010-hackny-fellows/)

2010

Google Student Award Winner, Machine Learning Symposium


The New York Academy of Sciences

2008

Jawaharlal Nehru Fellow


Jawaharlal Nehru Center for Advanced Scientific Research, Bangalore

2004

CONFERENCE TALKS
2015

Thousands of novel translated open reading frames identified using ribosome footprinting data Biology of Genomes, Cold Spring Harbor Laboratory, NY

2014

Accurate inference of causal variants in immune-related diseases using cell-type


specific functional genomic data ENCODE Consortium Meeting, Stanford, CA

2013

A hierarchical multiscale model to infer transcription factor occupancy from chromatin


accessibility data 63rd Annual meeting of the American Society of Human Genetics,
Boston, MA

2009

Fused SVM classification of temporal gene expression responses to endotoxin.


Annual meeting of the Society of Industrial and Applied Mathematics Student Days
Invited Talk

2008

An information-theoretic derivation of min-cut based graph partitioning 3rd Annual


Machine Learning Symposium, The New York Academy of Sciences, NY

CONFERENCE POSTERS
2015

Accurate inference of thousands of novel translated open reading frames and dually
coded regions using ribosome footprinting data 19th Annual International Conference
on Research in Computational Molecular Biology

2014

Accurate inference of regulatory domains and transcription factor binding elements


using chromatin accessibility data in multiple cell types Systems Biology: Global
Regulation of Gene Expression

2012

Inferring sparse multivariate models to predict disease phenotype from genotype 20th
Annual International Conference on Intelligent Systems for Molecular Biology

2010

Identifying hosts of families of viruses: a machine learning approach 5th Annual


Machine Learning Symposium, The New York Academy of Sciences

2010

Group sparsity in T-cell gene expression during the immune response 5th Annual
Machine Learning Symposium, The New York Academy of Sciences

2010

Optimization of the ordering of match questions on OKCupid 5th Annual


Machine Learning Symposium, The New York Academy of Sciences

2009

Fused SVM classification of temporal gene expression responses to endotoxin 4th


Annual Machine Learning Symposium, The New York Academy of Sciences

2008

An information-theoretic derivation of min-cut based graph partitioning Workshop on


Graph Cuts and Related Discrete or Continuous Optimization Problems, IPAM, UCLA

TEACHING EXPERIENCE
2009

Data-driven Modeling (Teaching Assistant)


Department of Applied Physics and Applied Mathematics, Columbia University

2008

Partial Differential Equations (Teaching Assistant)


Department of Applied Physics and Applied Mathematics, Columbia University

2011
2010
2006

Introduction to Biophysical Modeling (Teaching Assistant)


Department of Applied Physics and Applied Mathematics, Columbia University

2008
2005

Physics of Fluids (Teaching Assistant)


Department of Applied Physics and Applied Mathematics, Columbia University

REFERENCES
Dr. Jonathan Pritchard (postdoctoral adviser)
Investigator, Howard Hughes Medical Institute
Professor, Departments of Biology and Genetics, Stanford University

pritch@stanford.edu
Dr. Chris Wiggins (PhD adviser)
Chief Data Scientist, The New York Times
Associate Professor, Department of Applied Physics and Applied Mathematics, Columbia University
chris.wiggins@columbia.edu
Dr. Matthew Stephens
Professor, Departments of Human Genetics and Statistics, University of Chicago
mstephens@uchicago.edu

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